#1 It's a 5th gen with an extruder that has a long melt zone and for whatever reason- uses absurdly high default temps for printing PLA.
As such, we know that combination puts a LOT of heat into the PLA being extruded and that is extremely bad for rafts where we on purpose do not want a good layer bond.
I believe Makerware is either extruding the first layer of the actual object at a lower temp to prevent this extreme bonding or is using a taller than normal layer gap rise such that the first layer of the object has a nozzle height much higher than the actual layer height setting resulting in a poor bond. You can literally watch a makerware print job and see it do these things on the 5th gen. It pauses for a long time after printing the raft waiting for the fans to cool the extruder down.
#2 Pros look at rafts as training wheels. I mean it's just insane to me and anyone else experienced in this field- why in the world does the 5th generation- the crème of all knowledge learned after several years of making printers default to using rafts? I'll tell you why- the printer is junk and leveling and Z homing problems mean that first layer height is so variable and so unreliable, the raft is the method of compensation to mask the other major design issues of the printer.
#3 You asked a legit question, what can you do?
Decrease the temp of the raft layers, I don't have simplify 3D in front of me, but knowing you can per layer temperature setpoints in the temp tab of the profile.
You can also modify raft settings and try to duplicate how Makerware uses a greater gap for the first layer of the actual object.
The problem I really see here is- you bought S3D hoping to fix the very real hardware problems you may or may not have known about the 5th gen and that's a losing battle.
While I love S3D and think it's one of the most powerful slicers around- you simply cannot mask major design flaws and hardware issues with software.
The good news is- once you finally see the writing on the wall and get a different printer- S3D will work with that printer and you'll actually be able to use the "system" to it's fullest and enjoy the hobby.